LAMMPS (18 Jul 2015)
# 250 butane system for drude polarizability example (Langevin)

units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
special_bonds lj/coul 0.0 0.0 0.5

pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4

read_data data.butane
  orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  4500 atoms
  scanning bonds ...
  5 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  9 = max dihedrals/atom
  reading bonds ...
  4250 bonds
  reading angles ...
  6000 angles
  reading dihedrals ...
  6750 dihedrals
  5 = max # of 1-2 neighbors
  8 = max # of 1-3 neighbors
  12 = max # of 1-4 neighbors
  17 = max # of special neighbors

comm_modify vel yes

group gBUTANE molecule 1:250
4500 atoms in group gBUTANE
group gCORES type 1 2 3
3500 atoms in group gCORES
group gDRUDES type 4 5
1000 atoms in group gDRUDES

pair_coeff    1    1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
pair_coeff    1    2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H
pair_coeff    1    3 lj/cut/coul/long 0.044496 2.958040 # C3H H
pair_coeff    2    2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H
pair_coeff    2    3 lj/cut/coul/long 0.044496 2.958040 # C2H H
pair_coeff    3    3 lj/cut/coul/long 0.029999 2.500000 # H H
pair_coeff    *  4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
pair_coeff    1    * thole 1.368000
pair_coeff    2    * thole 1.368000
pair_coeff    4    * thole 1.368000
pair_coeff    5    * thole 1.368000

neighbor 2.0 bin

variable vTEMP   equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS  equal 1.0

velocity gCORES  create ${vTEMP} 12345
velocity gCORES  create 260 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345

fix fDRUDE all drude C C N D D

fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
  0 = # of size 2 clusters
  500 = # of size 3 clusters
  500 = # of size 4 clusters
  0 = # of frozen angles

fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
fix fNPH all nve

compute cTEMP all temp/drude

thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50

timestep 0.5
run 2000
PPPM initialization ...
  G vector (1/distance) = 0.367867
  grid = 36 36 36
  stencil order = 5
  estimated absolute RMS force accuracy = 0.031354
  estimated relative force accuracy = 9.44215e-05
  using double precision FFTs
  3d grid and FFT values/proc = 79507 46656
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 17
New max number of 1-2 to 1-4 neighbors: 17 (+0)
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  master list distance cutoff = 10
  ghost atom cutoff = 10
Memory usage per processor = 20.1567 Mbytes
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2] 
       0            0    6535.5187      2714.74    248.45112    3820.7787    3724.3278    140.75328    1.4735401            0   -518.77975    595169.42   -594696.41    -353319.1    55742.797    334.61375    18.435655 
      50    2.8944459    3475.1575    2067.5082    189.21692    1407.6493    846.00752    810.92425    115.58516            0   -764.28457    595242.38   -594842.96    3029.5187    55742.797    202.89871    152.54291 
     100    5.6009829    2975.2938    1988.4777    181.98411    986.81605    358.65377    931.63831    175.54125            0   -919.10691     595306.8   -594866.71    2010.6143    55742.797    231.36532    50.118891 
     150    8.2652578    2904.7202    1962.6821    179.62331    942.03808    234.91712    997.34884    195.22618            0   -909.31364    595293.23   -594869.37    4956.5664    55742.797    241.54715    14.313437 
     200     10.97319     2905.616     1909.813    174.78477    995.80302    228.33514    1082.3513    200.51771            0   -943.19777    595298.16   -594870.37    2973.6338    55742.797    238.34584    5.1137785 
     250    13.676164    2934.0626    1952.0155     178.6471     982.0471    212.76463    1131.5055    194.94566            0   -983.79846    595297.63      -594871    1591.8677    55742.797    244.66672    2.4161409 
     300    16.381759    2995.4781    2017.7772    184.66557    977.70088    213.25867    1133.9492    195.13329            0    -992.6543    595299.31   -594871.29    2817.7518    55742.797    253.21545    1.6812532 
     350     19.14905    3058.4882     1982.338     181.4222    1076.1502    228.54692    1197.9766    205.68279            0   -982.30502    595297.25      -594871    1408.2609    55742.797    248.83728    1.4672371 
     400    21.914272    3016.5895    1998.3531     182.8879    1018.2363    238.06518     1169.309    197.52924            0   -1014.8678    595298.98   -594870.78    1454.1926    55742.797     250.8778    1.3985907 
     450    24.629148     3014.232    1979.0496    181.12125    1035.1824    216.45567    1198.2831    197.81853            0   -1005.5029    595298.68   -594870.56    1296.2887    55742.797    248.44786    1.4025051 
     500    27.390589    3054.4694    2023.8824    185.22432     1030.587    220.97548    1197.2137    199.51957            0   -1014.3543    595298.28   -594871.05    2481.3102    55742.797    254.08894    1.4000969 
     550    30.147365    3088.0877    2020.1967      184.887    1067.8909    221.93439    1216.8427    213.27263            0   -1012.4867    595299.44   -594871.11    1697.8283    55742.797    253.63701    1.3687703 
     600    32.854639    3112.7966    2031.7038    185.94013    1081.0928    220.37419    1254.8806    208.09272            0   -1030.3329    595298.95   -594870.87   -75.358619    55742.797    255.05809     1.439614 
     650    35.725004    3155.4753    2025.6962    185.39031    1129.7792    221.82928    1284.1281    210.16702            0   -1015.1565    595299.63   -594870.82    1286.1601    55742.797    254.30974    1.4197689 
     700     38.70379    3134.5524    2054.9292     188.0657    1079.6232    225.36387    1243.5643    191.53984            0   -1010.9148    595301.25   -594871.18    700.78109    55742.797    257.97902    1.4421042 
     750    41.679769    3189.6098    2103.3042    192.49294    1086.3056     219.5641    1243.9772    203.81533            0   -1010.2161    595299.86    -594870.7    482.90086    55742.797    264.08828    1.3795515 
     800    44.637671    3173.7718    2053.4131    187.92694    1120.3587    219.52183    1256.8457    218.62858            0    -1003.175    595299.34   -594870.81     538.9293    55742.797    257.80398    1.4002525 
     850    47.531367    3221.5884    2084.0326    190.72922    1137.5559    224.32279    1277.7167    218.74781            0   -1011.3685    595298.54    -594870.4    145.40179    55742.797    261.66451    1.3777132 
     900    50.379314    3214.7916    2054.2398    188.00261    1160.5518    222.07439     1296.738     225.4151            0   -1013.6054    595300.61   -594870.68    490.09072    55742.797    257.90629    1.4047863 
     950    53.038527    3213.4974    2122.2134     194.2235     1091.284    221.85551    1252.3002    201.89089            0   -1014.1089    595300.04   -594870.69    1203.4321    55742.797    266.42418    1.4941572 
    1000    55.653448    3212.7244    2079.8287    190.34449    1132.8956    225.42816    1261.5078    204.71764            0   -986.95829    595298.68   -594870.48    790.47665    55742.797    261.10437    1.4611106 
    1050    58.290098    3216.1124    2106.2454    192.76212    1109.8669    213.54607    1261.1068    207.93437            0   -1001.5715    595299.05    -594870.2    69.145866    55742.797    264.43815    1.4332898 
    1100    60.921228    3218.0797    2082.4185     190.5815    1135.6611    236.95827    1266.8625    198.25038            0   -995.08857    595298.88    -594870.2    694.35787    55742.797    261.43907    1.4374087 
    1150    63.510285    3208.3968    2119.1968    193.94742       1089.2    210.20908    1236.1825    202.19163            0   -988.56762    595299.35   -594870.17    1528.4475    55742.797    266.08185    1.3950176 
    1200    66.140576    3219.1289     2078.071    190.18362    1141.0579    234.57015    1268.2146    206.93186            0   -997.01686    595298.32   -594869.97    939.70203    55742.797    260.89628    1.4263352 
    1250    68.774998    3268.5006    2115.3231     193.5929    1153.1775    241.50662    1262.3711    220.71001            0   -1000.1626    595298.37   -594869.62   -187.61926    55742.797    265.57695    1.4418423 
    1300    71.409732     3324.099    2138.7146    195.73368    1185.3844     242.3031    1279.7915    223.94399            0   -989.04901    595298.47   -594870.08    258.69655    55742.797    268.51674    1.4497832 
    1350    73.990336    3290.8471    2103.0993    192.47419    1187.7477    219.60844    1312.8653    221.57552            0   -993.69832    595297.61   -594870.21    1651.4259    55742.797    264.03877    1.4428477 
    1400    76.620059    3227.0141    2052.6998    187.86167    1174.3143    236.01325    1272.4804    217.65692            0    -979.6779     595297.5   -594869.66    595.11702    55742.797    257.67276    1.5108922 
    1450    79.249466    3253.5975     2107.984    192.92124    1145.6135    248.51645    1261.8304    208.79164            0   -1002.8333    595299.15   -594869.84    170.12671    55742.797    264.66781    1.4041436 
    1500    81.830899    3276.1976    2101.6206    192.33886     1174.577    242.38394      1288.61     204.9722            0    -989.7383    595298.02   -594869.67    619.26135    55742.797    263.84288    1.4691362 
    1550    84.449908    3271.9376    2117.6914    193.80965    1154.2463    234.62432    1268.5368    202.02117            0   -979.66071    595298.65   -594869.92    568.43047    55742.797    265.86458    1.4693675 
    1600    87.073373    3281.1387    2105.1447    192.66139     1175.994    219.69265    1288.3244    205.52796            0   -966.68015    595298.79   -594869.67    1351.6273    55742.797    264.27256    1.5056051 
    1650    89.695136     3287.675    2131.7955    195.10045    1155.8795    235.54527    1262.9178    220.26583            0   -991.68887    595298.56   -594869.72   -750.34342    55742.797    267.63101    1.4905169 
    1700    92.342235    3295.9626    2079.4982    190.31424    1216.4644    232.74928    1329.4691    218.51323            0   -992.04439    595297.16   -594869.38    589.94184    55742.797    261.06357    1.4590401 
    1750    94.911541    3315.2639    2097.2605    191.93983    1218.0035    241.24927    1312.3575    214.88139            0   -978.98823    595298.34   -594869.84   -92.971422    55742.797    263.26817    1.5389785 
    1800    97.525025    3241.5219    2086.8653    190.98847    1154.6566    221.03432    1282.1774    209.03793            0   -986.54668       595299   -594870.05    456.17335    55742.797    261.96332    1.5311996 
    1850    100.13804    3222.7069    2040.0335    186.70245    1182.6734    242.74754    1272.8794    221.80974            0   -982.51665    595296.99   -594869.24    279.00233    55742.797    256.09213    1.4766233 
    1900    102.70693    3190.3766    2032.3946    186.00335    1157.9819    213.06329     1268.187    220.21025            0   -971.50314    595297.54   -594869.51    499.15225    55742.797    255.16226    1.3935863 
    1950    105.30868    3208.3096    2053.9844    187.97923    1154.3252    212.46296    1277.2726    210.16078            0   -974.19087    595298.44   -594869.82    807.22906    55742.797    257.85261    1.4622515 
    2000     107.9105    3231.8811    2053.6913     187.9524    1178.1899    229.11239    1280.6492     220.1084            0   -979.25259    595297.02   -594869.45    474.05197    55742.797    257.80782    1.4833297 
Loop time of 107.911 on 1 procs for 2000 steps with 4500 atoms

Pair  time (%) = 65.8442 (61.0173)
Bond  time (%) = 16.6061 (15.3887)
Kspce time (%) = 20.7451 (19.2244)
Neigh time (%) = 1.24307 (1.15195)
Comm  time (%) = 0.386346 (0.358024)
Outpt time (%) = 0.00603366 (0.00559135)
Other time (%) = 3.07976 (2.854)

Nlocal:    4500 ave 4500 max 4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    8739 ave 8739 max 8739 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    860638 ave 860638 max 860638 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 860638
Ave neighs/atom = 191.253
Ave special neighs/atom = 13.3333
Neighbor list builds = 28
Dangerous builds = 0
